Pokemon: Return of the Shadows
by The Zelda Big Macintosh
Summary: They say that no pokemon is truly evil, that they just act according to their trainer's orders. But a new project by Cipher Corporation will prove that theory wrong. Now, it's up to a trio of young trainers to stop Cipher once and for all, before the world is plunged into the shadows.
1. Chapter 1: Even Villains Eat Lunch

**TZCN: I don't have anything clever to say about this rewrite. Just say the disclaimer. ...Paul? You're still on disclaimer duty! Get your butt out here!**

**Paul: Go screw yourself.**

**TZCN: Do I need to remind you of what I did to Drew?**

**Paul: Enlighten me.**

**TZCN: I put him in one of my specially made torture rooms.**

**Paul: What's so bad about that?**

**TZCN: They're filled with fanart of all the horrible pairings you can imagine, including Ikarishipping.**

**Paul: *goes pale* Dear God, not that! I'll, um, I'll get right on with it.**

**TZCN: Darn right you will.**

**Paul: TheZeldaChuckNorris owns nothing. So don't accuse him of plagiarism or he will block you like OathkeeperRoxaxXNamine did to him.**

**TZCN: I still don't see why he blocked me for trying to help. Hmph, that jerk. Anyway, story time.**

**Pokemon: Return of the Shadows**

**Chapter 1: Even Villains Eat Lunch **

Molly Hale smiled contentedly as she lay in the shade of the large oak tree, her cerulean eyes closed as her pokemon frolicked nearby. As the wind gently blew through her light brown hair in which she wore an indigo ribbon which matched her sleeveless dress which stopped just above her baby blue shoes, she couldn't help but turn her thoughts to one of the two boys out in the sun nearby setting up for their picnic lunch.

Max Maple. With short, midnight blue hair, a plain grass green t-shirt, black shorts, and crimson shoes, and a pair of circle rimmed glasses perched in front of his chocolate brown eyes, he was the handsomest boy Molly had ever seen back when they met in the new contest hall in Pewter City, and she quickly developed a crush on him. Of course, Tory was nice, but he already had girl problems as it was, what with Kaitlyn and Audrey from his hometown back in Hoenn both fawning over him.

Tory had shoulder length silver hair, forest green eyes, and wore a sky blue t-shirt with a silver neckline and sleeves and khaki jeans with plain white shoes.

"Molly, it's lunchtime!" Max called, breaking Molly from her thoughts.

She hurried over to the blanket that had been set out and sat down. Tory greeted her while Max ran out to gather the pokemon.

"Thinking about Max again?" he asked in a low whisper.

Molly blushed in embarrassment.

"N-no. W-why would you think that?" Molly answered.

Tory gave her a 'I'm not that stupid, you know' look before continuing.

"So, when are you planning on telling him you like him?" Tory asked again.

"T-that's none of your business!" Molly replied, blushing even harder and resisting the urge to slap the you-know-what out of the giggling trainer sitting next to her.

"What's so funny?" Max said, walking up to them, pokemon in tow.

"I think Molly should tell you." Tory answered.

Molly blushed again before quickly thinking of a joke.

"I, uh, told him a funny joke. Wanna hear it?" she asked?

"Sure! I love jokes!" Max replied.

"What do you call a popular snack that became a world renowned scientist?" Molly asked.

"I dunno. What?" Max said after thinking for a few moments.

"Sir Issac Fig Newton." Molly answered.

"Hahahaha! That's a good one!" Max laughed.

"Thanks." Molly said, quickly turning to hide her blush that came about from Max's compliment.

"Well then, let's eat!" Tory proclaimed.

"Alright!" Max replied.

And so the three friends and their pokemon proceeded to eat their lunch, joking and poking fun all the while. Soon they were finished, and they packed up and continued onwards towards Mt. Moon.

Meanwhile, on an island not far from Cinnabar Island that was thought to be deserted, a bunch of people in different colored body suits and helmets were standing outside of two large metal structures.

"Master Ardos. Construction on the base is finally complete." spoke one of them to a small device in his left hand.

"Well done, peon. I will be arriving in three weeks' time. I have sent an Admin ahead to keep order until then. Make sure absolutely nothing happens before my arrival." Ardos replied.

"Of course, Master Ardos." the peon answered.

"One more thing. Have you seen my father and/or brother at all?" Ardos asked.

"No sir. There's been no sighting of either of them since they fled Citadark Island five years ago." the peon answered again.

"Alright then. I leave you to hold down the base until the Admin arrives. Ardos out." Ardos replied one more time before breaking from the connection.

Far away in the Orre region, Ardos sat in the Krabby Cafe in Gateon Port. He smiled to himself.

'It won't be long now." he thought to himself, placing two fifties on the table before walking out.

**TZCN: What do you think? I worked hard on this. My writer's block is gone, and I am in gear. Hope you enjoyed, and I hope you enjoy the second chapter that is uploaded with this rewrite of the first! Hasta la vista, baby!**


	2. Chapter 2: To Mt Moon and Beyond!

**TZCN: It's time for...CHEEEAPTER TWO! ...That was uh, Chuggaaconroy. I was quoting Chuggaaconroy there. Anyway, disclaimer time.**

**Paul: TheZeldaChuckNorris owns nothing.**

**TZCN: Story time!**

**Chapter 2: To Mt. Moon and beyond!**

Max, Molly, and Tory were resting at the Pokemon Center outside the entrance to Mt. Moon. Max was looking over the Town Map.

"So once we're through Mt. Moon, we'll be right next to Cerulean City, where Tory and I can get our next badge and Molly can get her next ribbon. Then we need to head south through Saffron City to get to Vermilion City." Max explained.

"I can't wait to see Misty again! I'm so glad she and Ash are finally together!." Molly exclaimed.

"Believe me, Brock is happier than anyone, except maybe Ash and Misty themselves." Max laughed.

"I still laugh remembering how we saw him dancing around with glee with Misty's letter in his hands as we entered the Pewter City gym a few days ago." Molly replied, giggling, with Max soon joining in.

Tory simply smiled at the memory. He was keeping quiet and allowing Max and Molly to bond more. He didn't want to wait as long as Brock had for his traveling companions to hook up.

'Then again, Ash and Misty did fight a lot, compared to Max and Molly who get along perfectly fine.' Tory thought. He was brought out of his thoughts by Max.

"Tory, come on! We're heading out!" was the bespectacled boy's call.

"Coming!" Tory replied, grabbing his pokeballs off the counter and running to join his friends.

The three entered Mt. Moon, the sudden drop in lighting disorienting them for several moments before their eyes adjusted.

"Sure is dark in here. Hope we don't get lost." Max stated, his concerns clear in his tone of voice.

"Let's hold hands so we stay together." Tory suggested, smirking to himself when both Max and Molly stopped in their tracks.

"I...guess we could." Max muttered quietly.

"What about you Molly?" Tory asked the brunette.

"I guess so..." Molly replied.

"I guess I'll lead, then." Max said.

He extended his left hand behind him. Molly grasped it in her right hand, and extended her left back to Tory, who grabbed it with his left. The three continued walking as the cave grew darker. Soon, they could barely see.

"Man, it's so dark. Good thing Tory had the idea to hold hands." Max said.

"Y-yeah." Molly murmured.

"Something wrong, Molly?" Max asked.

"Huh? No. I, um, I'm just thinking about the upcoming contest in Cerulean is all. Nothing to worry about." Molly quickly responded.

"If you say so. Tory, you've been unusually quiet. Something wrong?" Max asked.

There was no reply.

"Tory?" Max called a bit louder.

This time, Tory responded with a "Huh?".

"You were being really quiet. I thought something might be wrong." Max answered.

"Oh. Well, I'm fine. I was just contemplating battle strategies. Since Plusle and Minun don't know any electric attacks yet, I need to plan out my strategy." Tory explained.

"Oh, alright." Max replied.

The trio continued on. Suddenly, it became too dark to see. The sudden surprise of the loss of vision made Molly gasp and, out of instinct, she squeezed Max's hand. Max blushed, glad that the sheer darkness of the cave meant no one could see it. Impulsively, he squeezed Molly's hand back. Like Max, Molly was grateful to the darkness for hiding her blush.

As the three young trainers trudged on, it soon became lighter, and lighter, until they reached the exit.

Tory let go of Molly's hand and ran out into the sunlight.

"Ah, fresh air, open space, and the ability to see more than three inches in front of me!" he exclaimed. He walked back to Max and Molly to find them still holding hands.

"Uh, guys? We're out of the cave now. You can let go of each other's hands." Tory said.

"Huh?" Both Max and Molly asked, before noticing that they had indeed neglected to release each other's hands after exiting Mt. Moon. They jumped apart, blushing.

"Uh, thanks, Tory." Max mumbled, before turning his attention to the road.

"On to Cerulean City!" he exclaimed with sudden enthusiasm.

"Yeah, let's go." Molly echoed.

The three of them took off for Cerulean, not knowing about the silhouettes of two men, one tall and lean, the other short and pudgy, watching them.

"They'll work." the taller one said.

"I hope you're right about this, Eldes." the short one replied.

"I'm sure, father." Eldes replied.

"Then let us continue to shadow them." the short man replied.

**TZCN: The plot thickens! I do so adore young love! If you've played Pokemon XD: Gale of Darkness, you'll know who the man with Eldes is. If you do, please _do not_ say who it is in the comments and spoil it for others. If you don't know who it is, wait and see. Hasta la vista, baby!**


	3. Chapter 3: Title Is Too Long

**TZCN: Time for chapter three, now with thirty percent more expected outcomes! Now, the disclaimer.**

**Paul: TheZeldaChuckNorris owns nothing.**

**TZCN: Story time ™!**

**Chapter 3: You Expected Different?**

"Ralts! Use Confuse Ray!" Max commanded.

"Ralts! Raaa-aaa-aaalts!" Ralts obeyed, sending a flash of psychich waves toward the opposing Starmie.

Starmie started flailing around, not knowing what it was doing, it's thoughts a blur. It was confused. Eventually, it wore itself out trying to figure out what was going on. As Starmie collapsed in a heap, its blinking core signifying it's exhausted state, Misty recalled it to its pokeball.

"Good try, Starmie. You gave it your best shot." Misty said to her pokeball before returning it to her scarlet backpack.

"Alright! We did it, Ralts!" Max cheered.

"Congratulations, Max. You've won the Cascade Badge." Misty said, handing Max a small badge shaped like a raindrop.

"Yes! I got the Cascade Badge!" Max yelled triumphantly, before stowing his new badge in his badge case next to a badge that looked similar to a boulder (**gee, I wonder why that is**).

"You remind me of myself when I was young." Ash remarked, walking over from where he, Molly, and Tory were spectating.

"Heh heh. I doubt I'll ever be as good as you though." Max replied.

"Ah, Max, you don't give yourself enough credit." Ash told him.

"Or maybe he gives you too much." Misty quipped, causing Ash to groan and Max to laugh at his friend's dismay.

"Mist, you never let me catch a break." Ash muttered, prompting said redhead to giggle.

"Well, we're out of here. See you all later. You'll be coming to watch Molly's contest, right?" Max asked.

"Wouldn't miss it." Ash answered, with Misty nodding in agreement.

"Alright then. Bye." Max ended as he, Molly and Tory headed outside of the gym.

Little did they know that the two men continued to watch them.

"Well, father?" Eldes asked.

"They certainly have potential. But it is too soon. They are still not strong enough yet. They must be given time to become stronger. Then, once their skills have sharpened enough, maybe they can be of use." the shorter man said.

"If you say so." Eldes replied.

"I do say so. Now let us be off." the short man said.

Many hours later, Max, Molly, Tory, Ash, and Misty are seen exiting the Cerulean City Contest Hall.

"Great job, Molly! You won your second ribbon!" Max congratulated.

Molly's cheeks turned pink, but she kept a straight face and turned to Max.

"Thanks, Max. I couldn't have done it without your support." Molly replied.

It was Max's turn to blush. Thankfully for him, he was saved from replying by Tory's interruption.

"Ahem." was the silver haired boy's statement.

"Thank you too, Tory." Molly playfully added.

Tory simply smirked.

"Well, it was nice seeing you guys again. But I gotta get home. Make sure and visit sometime." Ash said, before giving Misty a goodnight kiss and tossing out a pokeball. Out popped Charizard.

"Alright, Charizard. Let's go home." Ash told his pokemon.

Charizard gave a low growl of assent and knelt down to allow Ash to climb onto his back.

"Later guys." Ash called as Charizard took off for Pallet Town.

"I should be getting back home, too. See you three later. Good luck." she replied, winking at Molly.

Molly's cheeks turned pink again as she nodded.

"Uh, thanks. Goodbye." Molly answered.

"Bye." Misty called back before jogging off towards the gym.

"Ugh, I'm beat. Let's see if we can get a room at the Pokemon Center." Tory suggested.

"Good idea. I'm kinda exhausted. What about you, Molly?" Max asked.

"Yeah, I'm really tired after that tense final round of the contest. I could use a few hours of sleep." Molly answered, before yawning slightly.

"I'm sure our pokemon could use a rest, too. C'mon, let's go." Max stated as the three young trainers set off for the Pokemon Center in the southern area of town.

Once there, they checked their pokemon in for a rest-and-recover for the night, each paying for his or her own pokemon, and then retreated to the room they were assigned. Max flopped onto a bed, kicking his shoes off, removing his galsses, and laying back.

"Ahh. I could just fall asleep right now. Mmm, so comfy." Max commented.

Tory hopped onto the other bed after taking off his shoes, leaving Molly standing in the middle of the floor.

"Uh, guys? There's only two beds, and Pokemon Centers don't have roll-aways, and I definitely don't want to sleep on the floor ,so can I, um... can I share with one of you?" Molly asked before turning her head down in embarrassment.

"You can share with me, Molly." was what said girl heard.

Molly looked up to see Max smiling at her, holding out a hand. Max's smile making her go weak in the knees, Molly took Max's hand and let him help her onto the bed.

"T-thanks, Max." Molly said, feeling her face heat up.

"No problem. And, uh, I promise I won;t try anything...funny." Max answered

Molly was about to reply when she heard snoring. She and Max turned to find Tory already asleep. They turned back to each other, and shared a chuckle as Max got up, hit the light switch, and lay back down on the bed.

"Goodnight, Molly." Max said.

"Goodnight, Max." Molly answered.

The two trainers snuggled under the sheets and dirfted off to sleep.

**TZCN: There's chapter three for you! Hope you enjoyed and I hope you'll continue to read this story as I update it and continue to read my other stories as well. Thanks for reading.**


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